Rv3479 Resolved · high auto-curated
H37Rv Rv3479 · MTBC0 - ·
1021 aa · 3895820–3898885 (+) ·
RefSeq NP_217996.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane protein. Pfam: Patatin (PF01734.28), DUF3376 (PF11856.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06342
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized membrane protein Rv3479 |
UniProt still lists this protein as Uncharacterized membrane protein Rv3479; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3376) |
| Orthologous group | COG1752 |
| Gene Ontology (12) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0044425, GO:0044459, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.561 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 19 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (251) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Patatin | PF01734.28 | 2.7e-13 | 47–257 | Patatin-like phospholipase |
DUF3376 | PF11856.14 | 3.0e-26 | 606–697 | Protein of unknown function (DUF3376) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB5 (antitoxin VapB5), medium confidence from genomic context alone (score 604 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1947 hyp |
hypothetical protein | 652 | 653 ctx | cooccurence:646 |
Rv0626 vapB5 |
antitoxin VapB5 | 604 | 604 ctx | cooccurence:604 |
Rv0470A hyp |
hypothetical protein | 553 | 553 ctx | cooccurence:540 |
Rv1639c hyp |
hypothetical protein | 553 | 553 | coexpression:553 |
Rv0595c vapC4 |
ribonuclease VapC4 | 529 | 529 ctx | cooccurence:529 |
Rv0665 vapC8 |
ribonuclease VapC8 | 514 | 515 ctx | cooccurence:512 |
Rv3478 PPE60 |
PE family protein PPE60 | 487 | 487 ctx | neighborhood:471 |
Rv1995 hyp |
hypothetical protein | 464 | 464 ctx | cooccurence:464 |
Rv1775 hyp |
hypothetical protein | 444 | 444 ctx | cooccurence:431 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 431 | 432 ctx | cooccurence:431 |
Rv0355c PPE8 |
PPE family protein PPE8 | 424 | 425 ctx | cooccurence:421 |
Rv0341 iniB |
isoniazid inducible protein IniB | 444 | 424 ctx | cooccurence:406 |
Rv2209 |
integral membrane protein | 419 | 420 ctx | cooccurence:415 |
Rv3350c PPE56 |
PPE family protein PPE56 | 418 | 419 ctx | cooccurence:417 |
Rv3347c PPE55 |
PPE family protein PPE55 | 416 | 417 ctx | cooccurence:413 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transmembrane protein
- Pfam (hmmscan --cut_ga): Patatin PF01734.28 (E=3e-13), DUF3376 PF11856.14 (E=3e-26)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217996.2)
- Domains: Pfam-A via hmmscan --cut_ga — Patatin (PF01734.28), DUF3376 (PF11856.14)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1752 - Curated reference: UniProt O06342 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
19 functional partner(s); context anchor
vapB5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3479| MAGVTREINLLAQASQWRRLGGTFPTNSQLTNESAASLRLYAQLIDLLDMVVDVDILSGTSAGGINAALLASSRVTGSDLGGIRDLWLDLGALTELLRDPRDKKTPSLLYGDERIFAALAKRLPKLATGPFPPTTFPEAARTPSTTLYITTTLLAGETSRFTDSFGTLVQDVDLRGLFTFTETDLARPDTAPALALAARSSASFPLAFEPSFLPFTKGTAKKGEVPARPAMAPFTSLTRPHWVSDGGLLDNRPIGVLFKRIFDRPARRPVRRVLLFVVPSSGPAPDPMHEPPPDNVDEPLGLIDGLLKGLAAVTTQSIAADLRAIRAHQDCMEARTDAKLRLAELAATLRNGTRLLTPSLLTDYRTREATKQAQTLTSALLRRLSTCPPESGPATESLPKSWSAELTVGGDADKVCRQQITATILLSWSQPTAQPLPQSPAELARFGQPAYDLAKGCALTVIRAAFQLARSDADIAALAEVTEAIHRAWRPTASSDLSVLVRTMCSRPAIRQGSLENAADQLAADYLQQSTVPGDAWERLGAALVNAYPTLTQLAASASADSGAPTDSLLARDHVAAGQLETYLSYLGTYPGRADDSRDAPTMAWKLFDLATTQRAMLPADAEIEQGLELVQVSADTRSLLAPDWQTAQQKLTGMRLHHFGAFYKRSWRANDWMWGRLDGAGWLVHVLLDPRRVRWIVGERADTNGPQSGAQWFLGKLKELGAPDFPSPGYPLPAVGGGPAQHLTEDMLLDELGFLDDPAKPLPASIPWTALWLSQAWQQRVLEEELDGLANTVLDPQPGKLPDWSPTSSRTWATKVLAAHPGDAKYALLNENPIAGETFASDKGSPLMAHTVAKAAATAAGAAGSVRQLPSVLKPPLITLRTLTLSGYRVVSLTKGIARSTIIAGALLLVLGVAAAIQSVTVFGVTGLIAAGTGGLLVVLGTWQVSGRLLFALLSFSVVGAVLALATPVVREWLFGTQQQPGWVGTHAYWLGAQWWHPLVVVGLIALVAIMIAAATPGRR